Welcome to the forum Josh!
If you've read several threads about the motor mounts, there have been some people who replaced their mounts before their shaft broke. While they were glad to have gotten theirs done before having it break on the lake, they were then concerned about possible cracking due to the failed mounts and now their shaft was compromised and a ticking time bomb. Some people replaced them anyway just for the peace of mind.
All this to say, given your mounts were bad, it's not a bad idea to go ahead and replace the shaft too. It is surprising that your shaft broke in the shop and not on the water, but I'd try an get MB and your dealer to help you get it taken care of. I believe MB has been working with original owners to help them out. I'm not sure exactly what but give them a call. Hopefully they'll get you taken care of and you'll have the peace of mind knowing your mounts and shaft are all new.